title = 'methoxy decomposition to H + CH2O'

description = ''
frequencyScaleFactor = 1.0
"""
This example illustrates how to manually set up an Arkane input file for a small P-dep reaction system [using only the
RRHO assumption, and without tunneling, although this can be easily implemented]. Such a calculation is desirable if
the user wishes to supply experimentally determined frequencies, for example. Although some commented notes below may be
useful, see http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/index.html for more documented information
about Arkane and creating input files.
(information pertaining this file is adopted by Dames and Golden, 2013, JPCA 117 (33) 7686-96.)
"""
transitionState(
    label='TS3',
    E0=(34.1, 'kcal/mol'),  # this INCLUDES the ZPE. Note that other energy units are also possible (e.g., kJ/mol)
    spinMultiplicity=2,
    opticalIsomers=1,
    frequency=(-967, 'cm^-1'),
    modes=[  # these modes are used to compute the partition functions
        HarmonicOscillator(frequencies=([466, 581, 1169, 1242, 1499, 1659, 2933, 3000], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([0.970, 1.029, 3.717], "cm^-1"), symmetry=1, quantum=False),
        IdealGasTranslation(mass=(31.01843, "g/mol"))  # this must be included for every species/ts
    ],

)

transitionState(
    label='TS2',
    E0=(38.9, 'kcal/mol'),
    spinMultiplicity=2,
    opticalIsomers=1,
    frequency=(-1934, 'cm^-1'),
    modes=[
        HarmonicOscillator(frequencies=([792, 987, 1136, 1142, 1482, 2441, 3096, 3183], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([0.928, 0.962, 5.807], "cm^-1"), symmetry=1, quantum=False),
        IdealGasTranslation(mass=(31.01843, "g/mol"))
    ],

)
transitionState(
    label='TS1',
    E0=(39.95, 'kcal/mol'),
    spinMultiplicity=2,
    opticalIsomers=1,
    frequency=(-1756, 'cm^-1'),
    modes=[
        HarmonicOscillator(frequencies=([186, 626, 1068, 1234, 1474, 1617, 2994, 3087], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([0.966, 0.986, 5.253], "cm^-1"), symmetry=1, quantum=False),
        IdealGasTranslation(mass=(31.01843, "g/mol"))
    ],

)

species(
    label='methoxy',
    structure=SMILES('C[O]'),
    E0=(9.44, 'kcal/mol'),
    modes=[
        HarmonicOscillator(frequencies=([758, 960, 1106, 1393, 1403, 1518, 2940, 3019, 3065], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([0.916, 0.921, 5.251], "cm^-1"), symmetry=3, quantum=False),
        IdealGasTranslation(mass=(31.01843, "g/mol")),
    ],
    spinMultiplicity=3.88,  # 3+exp(-89/T)
    opticalIsomers=1,
    molecularWeight=(31.01843, 'amu'),
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
)

species(
    label='CH2O',
    E0=(28.69, 'kcal/mol'),
    molecularWeight=(30.0106, "g/mol"),
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
    spinMultiplicity=1,
    opticalIsomers=1,
    modes=[
        HarmonicOscillator(frequencies=([1180, 1261, 1529, 1764, 2931, 2999], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524], "cm^-1"), symmetry=2,
                       quantum=False),
        IdealGasTranslation(mass=(30.0106, "g/mol")),
    ],
)

species(
    label='H',
    E0=(0.000, 'kcal/mol'),
    molecularWeight=(1.00783, "g/mol"),
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
    modes=[
        IdealGasTranslation(mass=(1.00783, "g/mol")),
    ],
    spinMultiplicity=2,
    opticalIsomers=1,

)

species(
    label='CH2Ob',
    # this is a special system with two chemically equivalent product channels. Thus, different labels are used.
    E0=(28.69, 'kcal/mol'),
    molecularWeight=(30.0106, "g/mol"),
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
    spinMultiplicity=1,
    opticalIsomers=1,
    modes=[
        HarmonicOscillator(frequencies=([1180, 1261, 1529, 1764, 2931, 2999], 'cm^-1')),
        NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524], "cm^-1"), symmetry=2,
                       quantum=False),
        IdealGasTranslation(mass=(30.0106, "g/mol")),
    ],
)

species(
    label='Hb',
    E0=(0.0001, 'kcal/mol'),
    molecularWeight=(1.00783, "g/mol"),
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
    modes=[
        IdealGasTranslation(mass=(1.00783, "g/mol")),
    ],
    spinMultiplicity=2,
    opticalIsomers=1,

)
species(
    label='CH2OH',
    E0=(0.00, 'kcal/mol'),
    molecularWeight=(31.01843, "g/mol"),
    modes=[
        HarmonicOscillator(frequencies=([418, 595, 1055, 1198, 1368, 1488, 3138, 3279, 3840], 'cm^-1')),
        # below is an example of how to include hindered rotors
        # HinderedRotor(inertia=(5.75522e-47,'kg*m^2'), symmetry=1, barrier=(22427.8,'J/mol'), semiclassical=False),
        NonlinearRotor(rotationalConstant=([0.868, 0.993, 6.419], "cm^-1"), symmetry=1, quantum=False),
        IdealGasTranslation(mass=(31.01843, "g/mol")),
    ],
    spinMultiplicity=2,
    opticalIsomers=2,
    collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
)

species(
    label='He',
    #    freqScaleFactor = 1, # TypeError: species() got an unexpected keyword argument 'freqScaleFactor'.
    structure=SMILES('[He]'),
    molecularWeight=(4.003, 'amu'),
    collisionModel=TransportData(sigma=(2.55e-10, 'm'), epsilon=(0.0831, 'kJ/mol')),
    energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
    thermo=NASA(
        polynomials=[NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, -745.375, 0.928724], Tmin=(200, 'K'), Tmax=(1000, 'K')),
                     NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, -745.375, 0.928724], Tmin=(1000, 'K'), Tmax=(6000, 'K'))],
        Tmin=(200, 'K'), Tmax=(6000, 'K'), Cp0=(20.7862, 'J/(mol*K)'), CpInf=(20.7862, 'J/(mol*K)'), label="""He""",
        comment="""Thermo library: primaryThermoLibrary"""),
)

reaction(
    label='CH2O+H=Methoxy',
    #    label = 'Methoxy = CH2O+H',
    reactants=['CH2O', 'H'],
    products=['methoxy'],
    #    reactants = ['methoxy'],
    #    products = ['CH2O', 'H'],
    transitionState='TS3',
    # tunneling='Eckart',
)

reaction(
    #   label = 'CH2Ob+Hb=CH2OH',
    label='CH2OH = CH2Ob+Hb',
    #    products = ['CH2OH'],
    reactants=['CH2OH'],
    #   reactants = ['CH2Ob','Hb'],
    products=['CH2Ob', 'Hb'],
    transitionState='TS1',
    # tunneling='Eckart',
)

reaction(
    label='CH2OH = Methoxy',
    #    reactants = ['methoxy'],
    #    products = ['CH2OH'],
    #    label = 'Methoxy = CH2OH',
    products=['methoxy'],
    reactants=['CH2OH'],
    transitionState='TS2',
    # tunneling='Eckart',
)

kinetics('CH2O+H=Methoxy')
# kinetics('Methoxy = CH2O+H' )
# kinetics('Methoxy = CH2OH' )
kinetics('CH2OH = Methoxy')
kinetics('CH2OH = CH2Ob+Hb')
# kinetics('CH2Ob+Hb=CH2OH')
network(
    label='methoxy',
    isomers=[
        'methoxy',
        'CH2OH',
    ],

    reactants=[
        ('CH2O', 'H'),
        #        ('CH2Ob','Hb'),
    ],

    bathGas={
        'He': 1,
    },
)

pressureDependence(
    label='methoxy',
    Tmin=(450, 'K'), Tmax=(1200, 'K'), Tcount=4,
    Tlist=([450, 500, 678, 700], 'K'),
    Pmin=(0.01, 'atm'), Pmax=(1000, 'atm'), Pcount=7,
    Plist=([0.01, 0.1, 1, 3, 10, 100, 1000], 'atm'),
    maximumGrainSize=(0.5, 'kcal/mol'),
    minimumGrainCount=500,
    method='modified strong collision',
    # Other methods include: 'reservoir state', 'chemically-significant eigenvalues',
    interpolationModel='pdeparrhenius',
    activeKRotor=True,
    #    active_j_rotor = False,  # causes Arkane to crash
    rmgmode=False,
)
